How to remove a configuration in Eclipse GWT
Simply select any Web Application and click on RED X icon displayed on top right of it to remove an existing configuration.
Once a Web Application is configured then there is no need to create it again. Just launch it from existing one to avoid it choosing a launch configuration again.
Once configured then don't run it again by RIGHT click on the project to run as Web Application. Simply select from the existing one form the tool bar as shown in below screenshots.